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README
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$CTSMROOT/README 06/08/2018
Community Land Surface Model (CLM) science version 5.0.0 series -- source code, tools,
offline-build and test scripts. This gives you everything you need
to run CLM with CESM with datm8 to provide CRU NCEP or GSWP3 forcing data in
place of a modeled atmosphere.
For lists of current bugs (issues) and current development see the CTSM GitHub page:
https://github.com/ESCOMP/ctsm
IMPORTANT NOTE ON CESM CHECKOUT VERSUS A CTSM CHECKOUT:
If this is the top level directory from making a clone of CTSM the
directory structure is a little bit different than if CTSM is from
a clone of the entire CESM. If this is part of CESM this directory
will be under components/clm alongside other CESM component models.
For a CTSM checkout this will be the top level directory.
Other documentation will refer to $CTSMROOT and it means the directory
that this file is at. CIMEROOT is the directory where "cime" is for
this checkout. For a CESM checkout $CIMEROOT will be the "cime" directory
beneath the top level directory. For a CTSM checkout $CIMEROOT will
be $CTSMROOT/cime.
General directory structure ($CTSMROOT):
doc --------------- Documentation of CLM.
bld --------------- Template, configure and build-namelist scripts for clm.
src --------------- CLM Source code.
test -------------- CLM Testing scripts for CLM offline tools.
tools ------------- CLM Offline tools to prepare input datasets and process output.
cime_config ------- Configuration files of cime for compsets and CLM settings
manage_externals -- Script to manage the external source directories
python ------------ Some python modules mostly for use by run_sys_tests (but could be used elsewhere)
Directory structure only for a CTSM checkout:
components -------- Other active sub-components needed for CLM to run (river routing and land-ice models)
cime/scripts --------------- cesm/cime driver scripts
cime/src/drivers/mct/main ----------- CESM top level driver source code.
cime/src/drivers/mct/shr ------------ CESM top level driver shared code.
cime/src/components/data_comps/datm - CESM Data model version 8 source code.
cime/src/components/stub_comps/sice - CESM stub sea-ice model source code.
cime/src/components/stub_comps/socn - CESM stub ocean model source code.
cime/src/components/stub_comps/sglc - CESM stub glacier model source code.
cime/src/externals ------------------ CESM external utility codes
(Model Coupling Toolkit (MCT)
(Earth System Model Framework)
(timing -- code timing utility)
(pio -- Parallel Input/Output)
components/cism --------------------- CESM Community land Ice Sheet Model.
components/mosart ------------------- Model for Scale Adaptive River Transport
components/rtm ---------------------- CESM River Transport Model.
Top level documentation ($CTSMROOT):
README ------------------- This file
README.rst --------------- File that displays under the project in github
README_EXTERNALS.rst ----- Information on how to work with subversion externals for clm
CODE_OF_CONDUCT.md ------- Code of Conduct for how to work with each other on the CTSM project
Copyright ---------------- CESM Copyright file
doc/UpdateChangeLog.pl --- Script to add documentation on a tag to the
ChangeLog/ChangeSum files
doc/ChangeLog ------------ Documents different CLM versions
doc/ChangeSum ------------ Summary documentation of different CLM versions
doc/design --------------- Software Engineering and code design document files
Checklists for standard Software Engineering tasks
./doc/README.CHECKLIST.master_tags
./bld/namelist_files/README.CHECKLIST.interpolating_initial_conditions.md
Documentation of Namelist Items: (view the following in a web browser)
bld/namelist_files/namelist_definition_ctsm.xml --- Definition of all namelist items
bld/namelist_files/namelist_defaults_ctsm.xml ----- Default values
=============================================================================================
Important files in main directories (under $CTSMROOT):
=============================================================================================
Externals.cfg --------------- File for management of the main high level externals
Externals_CLM.cfg ----------- File for management of the CLM specific externals (i.e. FATES)
run_sys_tests --------------- Python script to send the standard CTSM testing off (submits
the create_test test suite for several different compilers on the
machines we do standard CTSM testing on).
parse_cime.cs.status -------- Script to parse test status files cs.status.* created by create_test
(can be used along with run_sys_tests)
doc/Quickstart.GUIDE -------- Quick guide to using cpl7 scripts.
doc/IMPORTANT_NOTES --------- Some important notes about this version of
clm, configuration modes and namelist items
that are not validated or functional.
doc/ChangeLog --------------- Detailed list of changes for each model version.
doc/ChangeSum --------------- Summary one-line list of changes for each
model version.
doc/README ------------------ Documentation similar to this file
doc/UsersGuide -------------- CLM Users Guide
doc/IMPORTANT_NOTES --------- Some important notes on caveats for some configurations/namelist items
bld/README ------------------ Description of how to use the configure and
build-namelist scripts.
bld/configure --------------- Script to prepare CLM to be built.
bld/build-namelist ---------- Script to build CLM namelists.
cime_config/buildnml ------------- Build the CLM namelist for CIME
cime_config/buildlib ------------- Build the CLM library
cime_config/config_compsets.xml -- Define CLM compsets
cime_config/config_component.xml - Define CLM XML settings
cime_config/config_tests.xml ----- Define CLM specific tests
cime_config/config_pes.xml ------- Define Processor layouts for various CLM grids and compsets
cime_config/testdefs ------------- Directory for specification of CLM testing
cime_config/testdefs/ExpectedTestFails.xml -- List of tests that are expected to fail
cime_config/usermods_dirs -------- Directories of sets of user-modification subdirs
(These are directories that add specific user modifications to
simulations created using "cime/scripts/create_newcase --user-mods-dir".
Current sub directories are for various CMIP6 configurations)
test/tools/test_driver.sh -- Script for general software testing of
CLM's offline tools.
tools/mksurfdata_map ---------- Directory to build program to create surface dataset
at any resolution.
tools/mkdatadomain ------------ Directory to build program to create datm7 or docn7
domain files from clm files.
tools/mkprocdata_map ---------- Process history data from unstructed grids to a gridded
format.
tools/mkmapgrids -------------- NCL script to create a SCRIP grid file for a regular lat/lon grid
tools/ncl_scripts ------------ Directory of NCL and perl scripts to do various
tasks. Most notably to plot perturbation error growth
testing and to extract regional information from
global datasets for single-point/regional simulations.
tools/contrib ----------------- Miscellansous useful scripts for pre and post processing
as well as case management of CTSM. These scripts are
contributed by users and may not be as well tested or
supported as other tools.
=============================================================================================
Source code directory structure:
=============================================================================================
src/biogeochem ---- Biogeochemisty
src/main ---------- Main control and high level code
src/cpl ----------- Land model high level MCT and ESMF drivers
src/biogeophys ---- Biogeophysics (Hydrology)
src/dyn_subgrid --- Dynamic land unit change
src/init_interp --- Online interpolation
scr/fates --------- FATES model and sub-directories
Functionally Assembled Terrestrial Ecosystem Simulator (FATES)
Experimental Ecosystem Demography model
src/utils --------- Utility codes
src/unit_test_shr - Unit test shared modules for unit testing
src/unit_test_stubs Unit test stubs that replicate CTSM code simpler
=============================================================================================
QUICKSTART: using the CPL7 scripts
=============================================================================================
cd $CIMEROOT/scripts
./create_newcase # get help on how to run create_newcase
./create_newcase --case testI --res f19_g17_gl4 --compset I2000Clm50BgcCrop
# create new "I" case for default machine at 1.9x2.5_gx1v7
# with 4km greenland ice sheetres resolution
# "I2000Clm50BgcCrop" case is clm5_0 active, datm8, and inactive ice/ocn
# With no-evolve ice-sheet, and MOSART for river-routing
cd testI
./case.setup # create the $CASE.run file
./case.build # build model and create namelists
./case.submit # submit script
# (NOTE: ./xmlchange RESUBMIT=10 to set RESUBMIT to number
# # of times to automatically resubmit -- 10 in this example)